Fix initialization without config

knossos-project / knossos_utils

Python library for interacting with KNOSSOS data sets and annotation files

GNU General Public License v2.0

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Fix initialization without config #23

Closed erjel closed 3 years ago

erjel commented 3 years ago

Fixed initialization of KnossosDataset with method initialize_without_conf

Causing problems:

glob wildcard * does not capture file separators.

Minor changes:

documentation does not specify boundary instance type. Added casting to numpy.Array
default parameter for mags causes error message. Added assertion to warn user.

Additional changes:

Added github workflow file for pytest do proof proper function.

my-tien commented 3 years ago

Hi, thanks for your pull request for those poorly maintained code locations! I have a few questions and will add them as comments to the individual commits.

erjel commented 3 years ago

@Optiligence , go ahead, I am happy to learn your approaches 😉

Optiligence commented 3 years ago

I integrated everything now.

I rearranged the changes a bit (e.g. removing net=0 changes) and adjusted some commit messages.

Your final commit (78418b33b3da4cd287b7ef302ae6ce12232709a4) changed the semantics and broke streaming. I resolved that differently and made the change clear in the commit message. lmk if how that works now, works for you.

fyi the new commits and the total diff.